His extended version at his blog: Microbiome Initial Data — I Need a Recount“Observationally, I have noticed several changes so far. First and best, is that my sleep has been incredible. I fall asleep easily, sleep through the night and wake up with a pep in my step. Second, my appetite is lower. I feel full all the time. My energy levels are good. There is marginal fluctuation throughout the day. Third, my poop is more regular both in consistency and frequency.”

Thank you Elijah for the generous introduction! I appreciate your enthusiasm and reaching out to me to collaborate on maximizing gut health and your 100 trillion friends.

Looking at uBiome stool analyses helps me to map out the bacterial terrain and landscape in the intestines. It is a ground breaking tool that I’m so grateful for. I look for landmarks and clues that tie in with published pyrosequencing studies.

Elijah is an elite athlete with superior performance and 8-9% body fat. I almost doubted that we could further improve any biometrics (sleep, skin, mood, performance), but, naturally, when we look at the modern dysbiotic gut, everything can be improved. Modern guts are particularly vulnerable because they are being assaulted from all sides everyday. Therefore several simple and easy improvements can dramatically reset overall health by emphasizing our gut.

Our gut is the initial site of nearly all disease (besides pure poisons). Our hunger, hormones, happiness chemicals and energy regulators all are controlled or composed by this master regulator organ that gut researchers call the ‘second brain’. Scientists report 80% of immunity is housed in the intestines. In my estimates, the gut doesn’t control all health, 24/7 all the time, but when it is disrupted, then ALL health may be disrupted. Whether you are an elite athlete like Elijah or a high-level executive or a super tiger-mom, a healthy gut lays the foundation for overflowing health, youthful energy, leanness and longevity.

Our modern lifestyles lend characteristic changes in the microbiome – depletions of vital good flora and overgrowths of opportunistic pathogens. I call the good microflora ‘gut guardians’ because these protect our gut from birth until death. Their absence signals death, whether it’s a slow, gradual, perpetual and mildly painful death or a more chronic course riddled by the common American standbys: cancer, cardiovascular disease, autoimmunity, joint degeneration, or diabetes-obesity.

Elijah’s gut profile exhibits the losses which everyone frequently experiences as a result of processed, refined carbohydrates, high sugar diets and use of antibiotics which were given for chronic ear infections as a child. His birth was C-section and studies show a lack of transfer of mom’s good microflora such as Bifidobacteria longum to baby without a vaginal birth.

Landmarks that stand out on Elijah’s gut microbiota uBiome analysis:

low biodiversity (low phyla and species counts)

depleted gut guardians which secure longevity and leanness by maintaining metabolism and a tight intestinal barrier

Faecalibacterium prausnitzii. In the side diagram, you can see how Elijah’s gut scored: doing well for producing butyrate, a fuel of the colonocytes, the cells that line the colon. Faecalibacterium prausnitzii is exuberantly represented. Most healthy humans have 3-10% or more and Elijah’s gut is no exception. His gut also houses plenty of Lachnospiraceae (34.64412%) and Pseudobutyrivibrio (8.86619%) This consortia of robust butyrate-producers may partly explain Elijah’s resistance to gaining fat and other dysbiosis-related disorders. Author of the Epidemic of Absence, Moises Velasqueze-Manoff, recently wrote an essay reviewing the vital anti-inflammatory role F. prausnitzii plays in protecting human health, ‘Among Trillions of Microbes in the Gut, a Few Are Special’.

Proteobacteria and other pathogens. A few potential opportunistic pathogens were identified. With gut guardians and allies, these easily overgrow at the first opportunity. Many of these may be gently weeded out and replaced by the populations missing, which will be stimulated by probiotics and special fiber. Normal skin microbiota residents are Staphylococcus, Corynebacterium (previously part of Corynebacteria), Propionibacterium, Streptococcus, and Pseudomonas. In acne, microbiota sequencing and culture studies show higher Corynebacteria, Staphylococcus epidermis, Propionibacterium acnes, and fungal Malassezia in skin lesions.

Our goal to improve the skin and work from the inside out, starting with shifting the gut microbiota, 100 trillion friends. This is also the progressive new thinking in dermatology:

“In the treatment of acne, one of the prevailing tenets has revolved around the eradication of a bacterium known as Propionibacterium acnes… Rather than non-specific chemical destruction of P. acnes, with its far reaching effects on the human microbiome, investigators are exploring the possibility of utilising non-pathogenic bacteria to improve the skin, with collateral benefits to the gastrointestinal tract and the psyche as well.”

With the lack of protection in the gut, bacterial and parasitic overgrowths may partially degrade the single-cell layer barrier in the small intestines (upper gut) where we absorb the vast majority of digested food and nutrients. Havoc and competition further lower the bacterial sentinels which everyday seal and maintain the barrier layer against being leaky and open.

An environment harmful for health ensues. Food and intestinal yeasts and bacteria may breach and ‘leak’ into the blood and lymph circulation which alarm the immune system, producing large amounts of silent inflammation which adverse affects many organ systems: liver, fat, and muscles. Instead of efficiently burning fat, the body burns other things, sugar and muscles.

The goals stated by Elijah are two-fold: (1) reverse intolerance to gluten which causes bloating and (2) improve mild acne on back

What we will do is enhance what the gut already has and repair-renovate what is broken. We discussed considering additions to the great smoothie blend that have been shown in humans to heal the gut and immunity rapidly (add 1-2 of the below). The below ‘feed and breed’ diversity in the gut microbiota including the specific species that are missing (Bifidobacteria longum, Akkermansia and Eubacteria).Choose a personal diverse combinational blend of prebiotic fiber:Elijah did all the below except GOS.

To seed-weed the proverbial gardens in our gut and crowd out modern potential pathogens, I often guide people to consider rebuilding the gut with health-promoting probiotics and gently weeding with short-term, combination botanicals. For skin I have a couple of tricks which speed healing in the gut. These would empirically target pathogens whilst specifically restructuring what is often missing. They all lower the quiet ‘fires’ of inflammation.

Elijah decided to go with all the above for the skin regimen and for probiotics decided on Bifidus Balance +FOS (Jarrow) and Primal Flora Ultra High Potency (Mark’s Daily Apple). The ability to breakdown casein (dairy) and gluten-gliadin (wheat) may come down to what is in our guts and what isn’t. The above probiotics contain strains which can help in digesting and degrading these potentially allergenic food peptides that induce food allergies, similar to what Elijah experiences. Primal Flora UHP is a soil based organisms probiotic (SBO) containing 10 billion CFU. Our recent ancestors had daily exposures to dust and dirt which contain these species. SBOs are one of the best ways to ‘seed’ the gut with bacteria aligned to our ancient past and better ability digest a range of plant fiber including small quantities of dairy and gluten.

I love Valasquez-Manoff’s use of the term “microbial ecosystem.” The more we talk about health and disease in gardening and ecosystem terms, the more we can increase our prevention tools.

Do you know what the “microbial ecosystem” of melanoma looks like? I know several people who have had melonoma/skin cancers. Some survived with brutal treatment; others did not. I note that I used to really cover-up in Florida: floppy hat, big cotton shirt. Still, I would get brown spots even if I just walked across the parking lot into a store. Since going PHD 2 years ago, I do not get brown spots anymore. I can even spend some time at the beach soaking up the sun on my face. I just turn pink with no lasting “age” spots. Might it mean less of a fungal load??

I wish I knew how the unique signatures for microbes in melanoma look like. I know several too — I feel sooo bad. That is so wonderful to hear about Paul Jaminent’s PHD diet!! His nutritional advice is very sound as well. Definitely some burden of silent inflammation has been reversed for you and the skin. Awesome!! If you have freckles I hope you don’t lose them all, I think they’re so cute.

I believe Paul and Tim Ferris were the early ones to really start improving the re-acceptance of complex carbohydrates into diets again. Game-changers. PHD is so rich in RS3 as well, the kind our ancient gut flora prefer for long, festive feasts!

The information you publish Dr. Grace is invaluable, but I get a bit annoyed about blanket recommendations on using inulin-FOS. I had a severe dysbiosis caused by klebsiella. I have regained balance through a lot of the recommendations for fiber, RS2 and RS3, but I find inulin-FOS fiber or even foods high in fructose to be very painful to my body, I asssume because of the klebsiella that must still have some grip on my body. I haven’t confirmed this with a stool test lately. Is there a particular weeding supplement that would be most effective against klebsiella? I am afraid of GFE, because I have heard how strong it is, and I don’t want to trigger my IBD.

You are right on — some Kleb will eat inulin-FOS/GOS and foods enriched in it (starchy roots, etc). That’s funny RS2 particularly feeds Kleb, in tender the uppergut.

Whether someone has Kleb or not, if the microvilli are denuded where the enzymes and dipeptidases for cleaving FODMAPs/inulin/FOS/GOS, then inulin will be problematic. Have you considered other ways to heal the barrier in the upper gut and avoidance of RS2 temp (or forever lol).

GFE is diff from grapeSEED extract.

Consider perhaps a couple of good tests to illuminate further what you are targeting — urine, stool, parasite/protozoa, yeasts etc

Hi Dr. Grace, thank you so much for your reply. The only RS2 I was really trying just lately was green banana starch, and I am not sure if I am handling it well yet so maybe I will stop it based on your comments. I do have no gluten or any grains in my diet, though I have considered quinoa, but try to have an R3 with every meal. I do the weed and feed, and fiber with probiotics you recommend. I know I need to do another stool test to see where I am at, but the extensive one you recommend (forgot the name) can only be done through doctors and I don’t have one that would order it. I am going to be adding Acacia fiber and the green powder next to my regime. I will probably try the GFE too, very slowly. I wanted to mention I have had a lot of good results with Chia Seed as a fiber, and I was hoping you might write something about it in the future. Best!

Maybe Eddie B will jump in — he recovered successfully from IBD. Yeasts and various opportunists are at the heart of IBD. They overgrow secondary to a lack of gut guardians — B longum in particular. Colorectal cancer is about 20-x higher in IBD and again this is likely secondary to a depletion of B longum which is found associated with nearly every Western disorder incl CRC and IBD.

B longum may sometimes actually be overgrown but in CRC and IBD, at the mucosa level it is dramatically depleted (and probably supplanted by yeasts and naught pathogens).

I like berberine and other botanicals. In studies berberine increases the vital B longum. Even green tea improves B longum and more importantly at the mucosa level of the small intestines.

Based on your research of the microbiome and any other health considerations you might want to take into account do you have an opinion about the ratio of animal protein from grass fed meats, fish and eggs, to other food sources like vegetables and legumes?

Macronutrient ratios may depend on various factors such as stage of gut healing/dysbiosis and then the person’s genetic makeup and health goals. Really had to make a generalized ratio or statement because we are all so unique and different!

Lisa and Savannahgreat question! Cocoa flavanols are great prebiotics, meaning they are food for the good gut flora such as lactobacilli and good bifidobacteria that keep us lean and strong, primarily Bifidobacteria longum and bifidum.

This study states below (the Eubacterium rectale group includes Roseburia, another ancestral core):

“We have previously shown that the flavanol monomer (+)-catechin significantly increases the growth of the Clostridium coccoides–Eubacterium rectale group, Bifidobacterium spp., and Escherichia coli, and significantly inhibits the growth of the Clostridium histolyticum group (25). Furthermore, tea phenolics have been shown to affect the growth of pathogenic bacteria such as Clostridium perfringens, Clostridium difficile, and Bacteroides spp. more than do commensal anaerobes such as Bifidobacterium spp. and Lactobacillus spp. (26). These data suggest that the consumption of flavanol-rich foods may have the potential to support gut health through their ability to exert prebiotic-like activity.”

“Daily HCF consumption also resulted in a significantly larger increase in the number of Bifidobacterium spp. in fecal samples collected postintervention (Figure 1), whereas no significant increase in the number of Bifidobacterium spp. was measured after the daily consumption of the LCF drink.”

C histolyticum is a potential pathogenic marker in the gut

“Interventions with HCF and LCF beverages for 4 wk led to a significant increase in numbers of the E. rectale–C. coccoides group, although there were no significant differences between the 2 groups. HCF consumption for 4 wk led to a significant decrease in the fecal numbers of the C. histolyticum group (P = 0.042), whereas LCF intake resulted in a significant increase in the fecal numbers of the C. histolyticum group (Figure 1). There was a significant difference in fecal amounts of the C. histolyticum group between the 2 intervention groups (P < 0.001).”

Lose your starch intake for Kleb. This includes unripe bananas and all root veges. You will just be feeding this particular bacteria with starch because it will provide food for Kleb all the way down past the ileocecal valve and into the ascending colon.

You will know kleb is an issue if you have extremely bad sleep. Also any symptoms of ankylosing spondylitis is another tell-tale sign of klebsiella overgrowth.

Grapefruit seed extract may help but this would be more beneficial on an empty stomach. I found lime juice (dependant on dilution) to be more effective. In vitro studies have indicated that lime is better than lemon, even.

Fruit fructose shouldn’t feed Klebsiella. Your malabsorption there could be more to do with leaky gut/SIBO issues.

Thank you so much for your thoughts, I can’t tell you how much it means to me. With Dr. Grace’s recent comments I have shut down the RS2’s but I am continuing the RS3’s. Ther Kleb overgrowth symptoms are spot on for me, difficulty sleeping, ankylosing spondylitis etc. With my ulcerative colitis (in remission) I have to tread delicately on things I add to my routine (foods and supplements) to prevent a flare and I have heard grapefruit seed extract is very effective against Kleb but harsh on the stomach. So I have been afraid to try it. I was going to try Tanalbit next to work on the Kleb, but I will try squeezing in a little lime with my fiber mix for a while. I guess I will just try to increase the amount of lime I drink gradually and see if that helps. Interesting to know that Kleb is not partly responsible for my fructose issues. I have been trying to supplement with bifido and R3’s hoping that may address some of the fructose malabsorption problems. All in all, I think I do a lot of good things diet wise and supplements because I am very disciplined, but it’s just a question of doing a better job of weeding successfully to give the good bacteria more room to flourish (I hope). Again, I thank you Chris and Dr. Grace for all your expert guidance!!

RS3 and digestible starches may also trigger until you address the Klebsiella depending on whether it has starch-degrading abilities or not. Inulin-FOS/GOS and fodmaps are a problem for some strains like K oxytoca (but usually no K pneumoniae).

We get Kleb from high sugar/grain diets, stress and the depletion of the gut guardians. Almost invariably yeasts/ candida are implicated in the overgrowths as well. Consider addressing both for optimal gut health. Thank you for your comments btrute.

These are past posts that address Klebsiella overgrowths which are often implicated in –autoimmune diseases like Hashimoto’s–obesity/diabetes/metabolic disorders–reactive arthritis–RA–ankylosing spondylitis–migraine headaches–colorectal cancer

What are your thoughts on the daily raw carrot that Ray Peat promotes to reduce overgrowth and toxins? He writes that it may actually work similar to clay in it’s ability to carry out excess growth, but I’m wondering where the carrot falls on the prebiotic spectrum. Is there resistant starch in the raw carrot or does it just act as more of an antimicrobial? I assume this is part of why people do well with a little carrot-beet-coconut oil concoction = antimicrobial, prebiotic, and liver promoting.

The paper you linked mentioned chitin-glucan to grow grow roseburia and ruminococcus, but it wasn’t clear where you get that and what else you can use. The description in the paper seemed to fit Artinia NAG, but that didn’t seem practical for this purpose. You also mentioned in a previous post that bifido help grow roseburia and ruminococcus.

Trying to balance out overgrowths and undergrowths without knocking anything else out of whack. I am high in odoribacter, prevotella, pseudoflavonifractor, f prausinitzii, oxalobacter, fusobacterium, and akkermansia. I am low in roseburia and ruminococcus and mid-range in bifido.

Anonymous

When you say choose 1-2 from below(for the fibre mix) do you mean 1 tsp of acacia and 1tbs of psyllium, for example? I’m just curious to know roughly what the total fibre intake in one go would be. I’m having a tough time digesting veggies so I’m temporarily depending mostly on supplements to fill that void.

On your last comment to btrute, you perfectly described the life of my disease. “We get Kleb from high sugar/grain diets, stress and the depletion of the gut guardians. Almost invariably yeasts/ candida are implicated in the overgrowths as well”

Do you know of any good studies or articles relating to biologic medicines and their effects on fungal/anti-fungal pathways?

I’ve read about it two separate times but I can’t remember where. I just remember that the comments weren’t in depth at all and lacked references.

Anonymous

Thank you Dr Grace for such a wonderful blog.

I’ve recently done a Geneva Comprehensive Profile stool test (Grace, I’ve forwarded you my test results). The good news is that my oxalobacter formigenes (decimated a few years ago by a strong round of antibiotics) have gone back!

For the not so good news, I’m still harbouring a few bandits: klebsiella pneumonia, hafnia alvei, and pseudomonas aeruginsa. I really don’t want to take the antibiotics route to weed these out and looking at the best alternative options. As I’m fairly lean (BMI 18.5, I’m a woman), would a low starch diet be such a good idea for me? Would a few weeks be enough time? MY diet is mostly PHD and a lot of my calories come from rice and root vegetables.

Actually with a very vibrant and robust gut, the unknowns can go up to 60-68% I’ve seen 😉

What we do know is key — the genera and order fall in line with known –mucin degraders*–acetic acid producers (vinegar makers)–lactate producers–other SCFA producers

The mucin degraders are the closest to the gut epithelium. Our health pivots on their presence and ubiome is good at identifying them along with potential opportunistic genera and the general ‘pattern’.

Do you have one? wanna send over?

Dee

Hello! I’d like to see if Grace or anyone around here may have any ideas for this…I’ve been prone to constipation all my life and it has gotten worse in the last year or so. Thing is the stool consistency is normal, not hard, and the stool is well formed. I eat a good variety of fiber, mainly from plants as i try to avoid grains as much as possible. I’m trying to introduce more fodmaps, but they do seem to give me some bloating, especially raw onions or garlic. I have a hard time just going, really. Even though the stool seems to be normal i rarely get the urge, so it’s like things are really slow. Could this be due to peristaltis? Does anyone else have this issue or any tips for this? Thank you.

I just got my results back, but I don’t see akkermansia anywhere in the raw taxonomy dump I downloaded. Does this mean they did not detect any? If I have none at all is it even possible to restore without a transplant? I’ve done antibiotics, RPS, and all the bad stuff you’re not supposed to do over the years.

Studies show that both Akkermansia and Bifidobacteria longum improve with straight oligosaccharides like GOS (Jarrow’s baby dophilus and Bimuno GOS). Foods that contain GOS are beans and lentils.

Good luck — I have the same issues. Too much potato starch ‘experimentation’ (WTF! #gerbilfood) and antibiotics. PS appears to lower Akkermansia by 10 to 20 fold despite recovery with different prebiotics in ubiome profile that I see. It takes time and nurturing of the flora that are nearly extinct.

B longum is its special ‘buddy’ and you need to recover both successfully.

The bad news is I was on bimuno and another GOS for 2 weeks before this sample, lognum was detected but at a measly 0.00182815%, ouch! I’ve taking prescript assist, vsl3 and various other probiotics in the past, but I never felt they gave a consistent benefit. Perhaps I should target just this strain.

Are the images with the blue background from a program that you put this data into, or did you generate those images yourself? I see the annotations and was curious if there is an additional resource I am missing.

I also wanted to ask if you put much weight into using your nose as a guide. I’ve noticed that GOS tends to make bowel movements smell like yogurt which must be the lactic acid bacteria being stimulated. If I take a lot of psyllium for a couple days I get a few foul smelling bowel movements followed by several weeks of low-odour, low-residue BMs. Usually a lot of gluten/dairy or junk food will undo that improvement. Apple pectin and this soluble fiber blend I take that has Psyllium seed husks, acacia gum, oat bran, apple fiber, and apple pectin extract seems to produce odourus BMs with no noticeable benefit. It makes me wonder if it’s doing more harm than good. If I eat apples they often pass through undigested, which is not typical of other fruits or foods I eat so I wonder if apple pectin is not good for me.

Is there merit to gravitating towards fibers and foods that produce “clean”, low-odor BMs? It seems intuitive that our nose would detect “bad” bacteria as smelling offensive and good bacteria as being neutral, but maybe it’s not as neat and straight forward as that.

SGeo

This may be out of your scope Dr. Grace, but is berberine safe while breastfeeding? I’m nursing a one-year-old and I really don’t want to stop. But I’ve been following the rest of your regimen and seeing amazing results. However, yeast has been my issue in the past, responsible for my skin issues, and I feel the berberine would be beneficial. I also feel like the healthier I am, the healthier my milk will be for my baby. What are your thoughts considering my daughter is an older baby and maybe less susceptible?

Noel

Dr Grace,

2 questions.
– The screenshots posted in this thread. I wonder which application that analysis was performed in. I have never seen such screen on uBiome’s website.
– Do you have suggested product links for the RS mix components you mentioned? I remember vaguely in one of the previous posts you linked all of those, but can’t find it now.

Miyarisan is a very interesting one — Clostridium butyricum — a butyric acid producer instead of a lactic acid producer.

DrGracePharmD-Gut_Goddess

Thank you so much Ken 😉 I’m glad you visited. For years I have enjoyed your concise and educational blog and it tremendously taught me about the CFS I had for several years.

I still use the Miyarisan from Shanghai (version) lol! Probiotic Clostridium is awesome. I’ve added different soil based probiotics into my kraut but don’t know if any really were extended! No butter tinged flavor, so who knows

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